The Whole Genome Sequencing Coverage Plot

Introduction

The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features

Dependencies

Software Version

• The tool is still in the development phases with current version is 1.0.0.dev0

Programming Languages

• Python (>=3.6)
• HTML/CSS/Javascript

Tools/libraries

• Echarts
• Python libraries: Biopython, rich, typer, pandas, requests
• select2
• jinja2

Installation

Install by pip

pip install wgscovplot

Install by conda

conda install -c bioconda wgscovplot

If the installation was successful, you should be able to type wgscovplot --help and get a help message on how to use the tool.

Usage

Usage: wgscovplot [OPTIONS]

Options:
 -s, --samples-data PATH         List of Sample Names, Coverage, VCF File
                                 [required]
 -o, --output-html PATH          Output Interactive HTML Coverage Plot
                                 [default: coverage_plot.html]
 -r, --ref-seq PATH              Reference genome sequences file  [required]
 -b, --bed PATH                  Bed file
 -g, --genbank PATH              Genbank file contains features of reference
                                 sequence  [required]
 --verbose / --no-verbose        Verbose logs  [default: no-verbose]
 --version / --no-version        Print wgscovplot version and exit
 --install-completion [bash|zsh|fish|powershell|pwsh]
                                 Install completion for the specified shell.
 --show-completion [bash|zsh|fish|powershell|pwsh]
                                 Show completion for the specified shell, to
                                 copy it or customize the installation.
 --help                          Show this message and exit.

Prepare Samples Data

The tool currently requires users to prepare samples data file (tsv file) is as the format below. We are updating the tool so that user just simply provide directory and file's identifiers

Note that no header is needed

Other data:

• Reference Sequences (reference.fasta)
• Genbank file contains gene features (sequence_genbank.gb)

Output:

The tool will generate the Coverage Plot for samples in HTML file

Command

wgscovplot -s samples.tsv -r reference.fasta -o sequencing_coverage_plot.html -g sequence_genbank.gb

Authors

• Development Lead: Peter Kruczkiewicz
• Software Developer: Hai Nguyen

License

Copyright 2021 Canadian Food Inspection Agency of Canada, Government of Canada.

Distributed under the MIT license.

What happens when the number of samples shown on the chart changed?

• By the default, at first up to 3 first samples are selected for displaying on the charts
• The entire chart will be re-rendered if you select/change samples to be displayed and you need to set your chart options again, changing other options will not re-render the entire chart

What happens when browser zoom is set more than 100%?

• Some minor graphic (such as some items get cut off) issues may happen. To fix this type of issue, try to adjust browser zoom and this may allow you to have better view

How many simultaneous samples are on the chart for the best view?

• It is recommended that having around 5 simultaneous samples on the chart for the best view

What will you do when the plot is distorted or minimized?

• This issue could happen when you shrink and maximize browser, to restore plot display just simply refresh browser